COLUMBIA – A federal judge has issued an order that dredging opponents say carries out the South Carolina Supreme Court’s cancellation of a permit a South Carolina agency issued last November.

“One of the key issues here is the U.S. Army Corps of Engineers has been threatening to short circuit the process and ignore South Carolina’s review,” Chris DeScherer, an attorney with the Southern Environmental Law Center, said Monday.

“This provides an opportunity for the parties to mediate a dispute, but it also ensures that the challenges brought by (environmental groups and the S.C. Savannah River Maritime Commission) will be heard and resolved in a timely fashion.”

Mediation involving former S.C. congressman John Spratt had been postponed ahead of the state Supreme Court decision, which was issued Friday.

In that decision, the court sided with environmental groups when it said the S.C. Department of Health and Environmental Control had no power to issue a 401 water quality certification to the corps last November. The certification refers to its section of federal Clean Water Act.

On Friday the state high court said the Savannah River Maritime Commission, a panel created by the S.C. Legislature in 2007 — not DHEC — wields the authority to award dredging permits on the river.

South Carolina lawmakers have attacked Georgia’s dredging plans on the grounds that it will put the Port of Charleston at a competitive disadvantage, damage the environment and eliminate the need for a shared Ga.-S.C. Jasper Ocean Terminal planned for a few miles closer to the ocean than the Savannah harbor.

The Southern Environmental Law Center filed suit, alleging the corps was supposed to obtain a permit under the S.C. Pollution Control Act in order to dump dredge spoils containing cadmium in Jasper County, S.C.

“Because the S.C. Supreme Court has ruled that no Clean Water Act certificate has now been issued, this court anticipates that the S.C. Pollution Control Act permit issue may be of some secondary importance at this time,” wrote U.S. District Judge Richard Gergel in the District of South Carolina Beaufort Division, in Monday’s order.

“These developments, which may both clarify some issues and raise new and difficult legal questions, suggest that this may be a propitious moment for the parties to sit down,” and try mediation, wrote the federal judge.

Gergel also told the corps to be forthcoming about its activities.

In a letter dated Oct. 26, days before the Supreme Court’s decision, the corps told U.S. Sen. Barbara Boxer, who chairs the Senate Committee on Environment and Public Works, that it is seeking an exemption from South Carolina’s 401 water quality requirement, “to prevent inappropriate delays” stemming from lawsuits.

In Monday’s order, Gergel told the corps to keep the court informed of such attempts. The judge ordered the corps to tell the court about any current and future submissions to Congress, seeking exemption from state permitting requirements.

In its Oct. 26 letter to Boxer, the corps had also said that if Congress authorizes the project or appropriates money for its construction, that amounts to an exemption.

Gergel’s order also directs the corps to share its funding picture with the court. He is calling for the corps to send a status report on federal appropriations for the $650 million deepening and to “promptly” update that report with any developments in the future.

The Georgia Ports Authority has been trying to deepen its channel from 42 feet to 47 feet, to get ready for larger ships traveling through the expanded Panama Canal in 2014.

“The project has been developed after more than a dozen years of expert study and analysis by multiple federal and state agencies,” Curtis Foltz, executive director for the Georgia Ports Authority said. “We remain confident that the project will move forward in accordance with all applicable authorities.”

On Monday evening, a corps spokesman said the agency is still reviewing the judge’s order.